"Damaged" fonts in pdf file after using TouchUp Text Tool

Hello,
I have a question regarding an issue with lost fonts in a pdf file.
The document was created in Adobe InDesign and printed to pdf.
However, after using the "TouchUp Text Tool" in order to check the font for a certain text, several attributes of the font have been damaged in the entire pdf: all characters in "small caps" have been transformed to regular.
We've had 3 cases so far.
Does anyone know how we can prevent this from happening again?
When exporting the document to pdf, all fonts were embedded, I am not sure if this can be the cause.
Thank you in advance for any suggestions!
Paula

We are using Adobe 8 Professional.
Bill@VT, I am not sure what you are asking me
I have checked the Preferences for the pdf file and the "Use system fonts" case is checked.
When opening the pdf file, the fonts were ok, but somewhere along the process, the small caps were lost.
Maybe a print screen will be of use: the presentation above is the correct presentation (the one immediately after exporting to pdf); the presentation below is the one after all fonts were damaged.

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